Tilo Buschmann
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/DNABarcodes |
| git_branch: RELEASE_3_19 |
| git_last_commit: 898712c |
| git_last_commit_date: 2024-04-30 10:45:46 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 596/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Tilo Buschmann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the DNABarcodes package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DNABarcodes.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: DNABarcodes |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DNABarcodes_1.34.0.tar.gz |
| StartedAt: 2024-06-09 20:04:28 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 20:05:43 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 75.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DNABarcodes.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DNABarcodes_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/DNABarcodes.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNABarcodes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DNABarcodes’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DNABarcodes’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
First development version for introduction to Bioconductor
Cannot process chunk/lines:
This is the first public release.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
create.dnabarcodes 6.201 0.096 7.034
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/DNABarcodes.Rcheck/00check.log’
for details.
DNABarcodes.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DNABarcodes ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘DNABarcodes’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DNABarcodes_init.c -o DNABarcodes_init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c analyse_barcodes.cpp -o analyse_barcodes.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c barcode_set_distances.cpp -o barcode_set_distances.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cachedistance.cpp -o cachedistance.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromosome.cpp -o chromosome.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c code_falsification.cpp -o code_falsification.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c conway.cpp -o conway.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c create_distance_func.cpp -o create_distance_func.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c create_dnabarcodes.cpp -o create_dnabarcodes.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c create_pool.cpp -o create_pool.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c demultiplex.cpp -o demultiplex.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distance_for_R.cpp -o distance_for_R.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genericchromosome.cpp -o genericchromosome.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c greedyevolution.cpp -o greedyevolution.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hammingdistance.cpp -o hammingdistance.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c helpers.cpp -o helpers.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c levenshteindistance.cpp -o levenshteindistance.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phaseshiftdist.cpp -o phaseshiftdist.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sequence.cpp -o sequence.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sequencepool.cpp -o sequencepool.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o DNABarcodes.so DNABarcodes_init.o RcppExports.o analyse_barcodes.o barcode_set_distances.o cachedistance.o chromosome.o code_falsification.o conway.o create_distance_func.o create_dnabarcodes.o create_pool.o demultiplex.o distance_for_R.o genericchromosome.o greedyevolution.o hammingdistance.o helpers.o levenshteindistance.o maxclique_pattabiraman_heuristic.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o sequencepool.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-DNABarcodes/00new/DNABarcodes/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'DNABarcodes' is deprecated and will be removed from Bioconductor version 3.20 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'DNABarcodes' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (DNABarcodes)
DNABarcodes.Rcheck/DNABarcodes-Ex.timings
| name | user | system | elapsed | |
| DNABarcodes-package | 1.141 | 0.022 | 1.253 | |
| analyse.barcodes | 0.009 | 0.010 | 0.044 | |
| barcode.set.distances | 0.021 | 0.016 | 0.075 | |
| create.dnabarcodes | 6.201 | 0.096 | 7.034 | |
| create.pool | 0.025 | 0.060 | 0.150 | |
| demultiplex | 1.541 | 0.418 | 2.136 | |
| distance | 0.001 | 0.000 | 0.001 | |